Abstract: The stimulatory effects of atmospheric pressure cold plasma (APCP) on plant growth have attracted much attention due to its great potential as a new approach to increase crop growth and production. However, the transcriptome changes of plants induced by APCP treatment are unknown. Herein, the comparative transcriptome analysis was performed to identify the transcriptional response of Arabidopsis thaliana seedlings to APCP. Results showed that APCP exhibited a dual effect (stimulation or inhibition) on Arabidopsis seedling growth dependent on the treatment time and the maximum stimulatory effects were achieved by 1 min APCP treatment. The metabolic analysis of amino acid, glutathione (GSH) and phytohormone demonstrated that 1 min APCP treatment decreased most amino acids concentrations in Arabidopsis seedling, while the accumulations of GSH, gibberellins and cytokinin were significantly increased. The RNA-Seq analysis showed that a total of 218 differentially expressed genes (DEGs) were identified in 1 min APCP-treated seedlings versus the control, including 20 up-regulated and 198 down-regulated genes. The DEGs were enriched in pathways related to GSH metabolism, mitogen-activated protein kinase (MAPK) signaling transduction and plant resistance against pathogens. Moreover, most of the DEGs were defense, stimuli or stress-responsive genes and encoded proteins with oxidoreductase activity. Expression determination of six randomly selected DEGs by quantitative real-time PCR demonstrated similar pattern with the RNA-Seq data. These results indicated that the moderate APCP treatment may regulate the expression of stimuli/stress-responsive genes involved in GSH, phytohormone/amino metabolism and plant defense against pathogens via MAPK signal transduction pathway, accordingly enhance Arabidopsis seedling growth. This study provides a theoretical basis for the application of APCP in agriculture.